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- ItemNFDI4Chem - A Research Data Network for International Chemistry(Berlin : De Gruyter, 2023) Steinbeck, Christoph; Koepler, Oliver; Herres-Pawlis, Sonja; Bach, Felix; Jung, Nicole; Razum, Matthias; Liermann, Johannes C.; Neumann, SteffenResearch data provide evidence for the validation of scientific hypotheses in most areas of science. Open access to them is the basis for true peer review of scientific results and publications. Hence, research data are at the heart of the scientific method as a whole. The value of openly sharing research data has by now been recognized by scientists, funders and politicians. Today, new research results are increasingly obtained by drawing on existing data. Many organisations such as the Research Data Alliance (RDA), the goFAIR initiative, and not least IUPAC are supporting and promoting the collection and curation of research data. One of the remaining challenges is to find matching data sets, to understand them and to reuse them for your own purpose. As a consequence, we urgently need better research data management.
- ItemAn environment for sustainable research software in Germany and beyond: current state, open challenges, and call for action(London : F1000 Research Ltd, 2021) Anzt, Hartwig; Bach, Felix; Druskat, Stephan; Löffler, Frank; Loewe, Axel; Renard, Bernhard Y.; Seemann, Gunnar; Struck, Alexander; Achhammer, Elke; Aggarwal, Piush; Appel, Franziska; Bader, Michael; Brusch, Lutz; Busse, Christian; Chourdakis, Gerasimos; Dabrowski, Piotr Wojciech; Ebert, Peter; Flemisch, Bernd; Friedl, Sven; Fritzsch, Bernadette; Funk, Maximilian D.; Gast, Volker; Goth, Florian; Grad, Jean-Noël; Hegewald, Jan; Hermann, Sibylle; Hohmann, Florian; Janosch, Stephan; Kutra, Dominik; Linxweiler, Jan; Muth, Thilo; Peters-Kottig, Wolfgang; Rack, Fabian; Raters, Fabian H. C.; Rave, Stephan; Reina, Guido; Reißig, Malte; Ropinski, Timo; Schaarschmidt, Joerg; Seibold, Heidi; Thiele, Jan P.; Uekermann, Benjamin; Unger, Stefan; Weeber, RudolfResearch software has become a central asset in academic research. It optimizes existing and enables new research methods, implements and embeds research knowledge, and constitutes an essential research product in itself. Research software must be sustainable in order to understand, replicate, reproduce, and build upon existing research or conduct new research effectively. In other words, software must be available, discoverable, usable, and adaptable to new needs, both now and in the future. Research software therefore requires an environment that supports sustainability. Hence, a change is needed in the way research software development and maintenance are currently motivated, incentivized, funded, structurally and infrastructurally supported, and legally treated. Failing to do so will threaten the quality and validity of research. In this paper, we identify challenges for research software sustainability in Germany and beyond, in terms of motivation, selection, research software engineering personnel, funding, infrastructure, and legal aspects. Besides researchers, we specifically address political and academic decision-makers to increase awareness of the importance and needs of sustainable research software practices. In particular, we recommend strategies and measures to create an environment for sustainable research software, with the ultimate goal to ensure that software-driven research is valid, reproducible and sustainable, and that software is recognized as a first class citizen in research. This paper is the outcome of two workshops run in Germany in 2019, at deRSE19 - the first International Conference of Research Software Engineers in Germany - and a dedicated DFG-supported follow-up workshop in Berlin.
- ItemThe openCARP CDE: Concept for and implementation of a sustainable collaborativedevelopment environment for research software(Marburg : Philipps-Universität, 2022) Bach, Felix; Klar, Jochen; Loewe, Axel; Sánchez, Jorge; Seemann, Gunnar; Huang, Yung-Lin; Ulrich, RobertThis work describes the setup of an advanced technical infrastructure for collabora-tive software development in large, distributed projects based on GitLab. We presentits customization and extension, additional features and processes like code review,continuous automated testing, DevOps practices, and sustainable life-cycle manage-ment including long-term preservation and citable publishing of software releasesalong with relevant metadata. The collaborative development environment (CDE) iscurrently used for developing the open cardiac simulation software openCARP and anevaluation showcases its capability and utility for collaboration and coordination ofsizeable heterogeneous teams. As such, it could be a suitable and sustainable infras-tructure solution for a wide range of research software projects.
- ItemNFDI4Chem - Fachkonsortium für die Chemie(Marburg : Philipps-Universität, 2021) Ortmeyer, Jochen; Schön, Florian; Herres-Pawlis, Sonja; Jung, Nicole; Bach, Felix; Liermann, Johannes; Neumann, Steffen; Popp, Christian; Razum, Matthias; Koepler, Oliver; Steinbeck, ChristophAls Fachkonsortium für die Chemie hat sich NFDI4Chem innerhalb der Nationalen Forschungsdateninfrastruktur (NFDI) gebildet. In diesem Beitrag stellt sich das Konsortium kurz vor und legt seine zentralen Ziele und wichtigsten Verbesserungen für das Forschungsdatenmanagement (FDM) in der Chemie sowie die praktischen Heraus-forderungen dar. Die Vision von NFDI4Chem ist die umfassende Digitalisierung und Vernetzung aller Prozesse im Umgang mit Forschungsdaten in der chemischen Forschung. Beginnend mit der Erzeugung der Daten, über deren Verarbeitung und Analyse bis hin zur Publikation wird eine modulare, vernetzte Infrastruktur aus Software-Tools, elektronischen Laborjournalen und Datenrepositorien entwickelt und bereitgestellt, die Forschende im Laboralltag unterstützt. Die Digitalisierung wird begleitet durch die Entwicklung von Minimalinformationen für Datenpublikationen, bestehend unter anderem aus Standards für Daten- und Metadatenformate sowie Ontologien zur semantischen Beschreibung. Seine Aufgaben verfolgt das NFDI4Chem-Konsortium wissenschaftsgeleitet und mit dem klaren Ziel, eine intuitiv und effizient nutzbare Infrastruktur zu entwickeln. Das Gestalten eines kulturellen Wandels, gemeinsam mit der wissenschaftlichen Community, zur Etablierung und Akzeptanz eines FAIRen Umgangsmit Daten ist daher ein weiteres wichtiges Element der NFDI4Chem-Aktivitäten.
- ItemNFDI4Chem - Deliverable D3.3.1: Gap analysis report for selected repositories(Genève : CERN, 2023) Bach, Felix; Binder, Kunigunde; Christian Bonatto, Minella; Lutz, Benjamin; Razum, MatthiasThe deliverable 3.3.1 “Gap analysis report for selected repositories” aims both to identify gaps in the coverage regarding data types or disciplines and to close them through adjustments or, if necessary, new developments. In order to accomplish that, the TA3-team performed a gap analysis of the existing relevant repositories by means of individual interviews with the repository leaders. The interview consisted of a series of questions ranging from general information up to metadata standards and ontology, data contents, technical information about Authorisation and Authentication Infrastructure (AAI), API, services and functionality, operating environment as well as software architecture and workflows. The interviews will serve to establish the current degree of maturity as well as the operational fitness of the selected repositories and to derive suitable recommendations aiming to fulfil the yet missing requirements.
- ItemHarmonising, Harvesting, and Searching Metadata Across a Repository Federation(Hannover : TIB Open Publishing, 2023) Neumann, Steffen; Bach, Felix; Castro, Leyla Jael; Fischer, Tillmann; Hofmann, Stefan; Huang, Pei-Chi; Jung, Nicole; Katabathuni, Bhavin; Mauz, Fabian; Meier, René; Nainala, Venkata Chandra Sekhar; Rayya, Noura; Steinbeck, Christoph; Koepler, OliverThe collection of metadata for research data is an important aspect in the FAIR principles. The schema.org and Bioschemas initiatives created a vocabulary to embed markup for many different types, including BioChemEntity, ChemicalSubstance, Gene, MolecularEntity, Protein, and others relevant in the Natural and Life Sciences with immediate benefits for findability of data packages. To bridge the gap between the worlds of semantic-web-driven JSON+LD metadata on the one hand, and established but separately developed interface services in libraries, we have designed an architecture for harmonising, federating and harvesting metadata from several resources. Our approach is to serve JSON+LD embedded in an XML container through a central OAI-Provider. Several resources in NFDI4Chem provide such domain-specific metadata. The CKAN-based NFDI4Chem search service can harvest this metadata using an OAI-PMH harvester extension that can extract the XML-encapsulated JSON+LD metadata, and has search capabilities relevant in the chemistry domain. We invite the community to collaborate and reach a critical mass of providers and consumers in the NFDI.
- ItemRADAR: Building a FAIR and Community Tailored Research Data Repository(Hannover : TIB Open Publishing, 2023) Bach, Felix; Soltau, Kerstin; Göller, Sandra; Bonatto Minella, Christian; Hofmann, StefanThe research data repository RADAR is designed to support the secure management, archiving, publication and dissemination of digital research data from completed scientific studies and projects. Developed as a collaborative project funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) (2013-2016), the system is operated by FIZ Karlsruhe - Leibniz Institute for Information Infrastructure - and currently serves as a generic cloud service for about 20 universities and non-university research institutions. Since its launch, RADAR has witnessed significant changes in the landscape of research data repositories and the evolving needs of researchers, research communities and institutions. In our presentation within the “Enabling RDM” Track, we will show how RADAR is responding to these dynamic changes. In order to create a sufficiently large user base for the sustainable operation of the system, we have moved RADAR away from its previous single focus on a discipline-agnostic cloud service and towards a demand-driven functional optimisation. In 2021, we introduced an additional operating model for institutions (RADAR Local), where we operate a separate RADAR instance locally at the institution site exclusively using the institutional IT-infrastructure. In 2022 we opened up RADAR to new target groups with community-specific service offerings, in particular in the context of the National Research Data Infrastructure (NFDI). Beside the expansion of the functional scope, our ongoing development work focuses also on strengthening the system's support for the FAIR principles [1] and the concepts of FAIR Digital Objects (FDO) [2] and Schema.org. Our presentation will outline recent RADAR developments and achievements as well as future plans thus providing solutions and synergy potential for the scientific community and for other service providers.
- ItemDigitalizing the Chemical Landscape: A Comprehensive Overview and Progress Report of NFDI4Chem(Hannover : TIB Open Publishing, 2023) Koepler, Oliver; Steinbeck, Christoph; Bach, Felix; Herres-Pawlis, Sonja; Jung, Nicole; Liermann, Johannes; Neumann, Steffen; Razum, MatthiasThe Chemistry consortium NFDI4Chem aims to digitalise key steps in chemical research, supporting scientists in managing research data throughout its life cycle. The SmartLab, embedded in a federation of services, integrates various tools such as electronic lab notebooks, data repositories, and search services, to create a smart lab environment for structured data gathering. Utilizing terminology services and adhering to data format standards, NFDI4Chem promotes secure and FAIR data sharing, fostering collaboration and expediting scientific discoveries. This development is supported by community building measures, workshops, and training initiatives, along with collaboration on international minimum information standards.
- ItemThesenpapier Nationale Forschungsdateninfrastruktur für die Chemie (NFDI4Chem)(Zenodo, 2018) Koepler, Oliver; Jung, Nicole; Kraft, Angelina; Neumann, Janna; Auer, Sören; Bach, Felix; Bähr, Thomas; Engel, Thomas; Kettner, Carsten; Kowol-Santen, Johanna; Liermann, Johannes; Lipp, Anne; Porzel, Andrea; Razum, Matthias; Schlörer, Niels; Solle, Dörte; Winkler, Torsten“Der stufenweise Aufbau einer Nationalen Forschungsdateninfrastruktur in Netzwerkform hat das Ziel, ein verlässliches und nachhaltiges Dienste-Portfolio zu schaffen, welches generische und fachspezifische Bedarfe des Forschungsdatenmanagements in Deutschland abdeckt.” Für das Fachgebiet Chemie ermöglicht eine solche nationale Forschungsdateninfrastruktur, öffentlich-finanzierte Forschungsdaten effizient zu erheben, standardisiert zu beschreiben, dauerhaft zu speichern und durch Persistent Identifier (PID) eindeutig referenzierbar und auffindbar zu machen. Sie unterstützt gemäß den Vorgaben des RfII die Reproduzierbarkeit und Nachnutzbarkeit der Daten zum Zwecke einer perpetuierten Wissensgenerierung. Mit der Reproduzierbarkeit von Forschungsergebnissen unterstützt eine solche Forschungsdateninfrastruktur den Peer Reviewing Prozess zur Förderung der wissenschaftlichen Selbstkontrolle und erhöht die Datenqualität, insbesondere in wissenschaftlichen Publikationen. Die NFDI4Chem ist ein gemeinschaftlicher Ansatz von Wissenschaftlern aus der Chemie, der Fachgesellschaft Gesellschaft Deutscher Chemiker und deren Fachgruppen, Einrichtungen aus der Forschungsförderung und Infrastruktureinrichtungen (Technische Informationsbibliothek). Eine Gruppe von Vertretern dieser Stakeholder hat sich Ende April 2018 zu einem Auftakttreffen “Fachgespräch NFDI4Chem” in Hannover getroffen. Dieses Papier fasst die Erkenntnisse des Fachgespräches zusammen. Weitere Stakeholder wie Verlage oder Datenbankanbieter sind im folgenden Diskurs willkommen.
- ItemConcept for Setting up an LTA Working Group in the NFDI Section "Common Infrastructures"(Zenodo, 2022-04-12) Bach, Felix; Degkwitz, Andreas; Horstmann, Wolfram; Leinen, Peter; Puchta, Michael; Stäcker, ThomasNFDI consortia have a variety of disparate and distributed information infrastructures, many of which are as yet only loosely or poorly connected. A major goal is to create a Research Data Commons (RDC) . The RDC concept1 includes, for example, shared cloud services, an application layer with access to high-performance computing (HPC), collaborative workspaces, terminology services, and a common authentication and authorization infrastructure (AAI). The necessary interoperability of services requires, in particular, agreement on protocols and standards, the specification of workflows and interfaces, and the definition of long-term sustainable responsibilities for overarching services and deliverables. Infrastructure components are often well-tested in NFDI on a domain-specific basis, but are quite heterogeneous and diverse between domains. LTA for digital resources has been a recurring problem for well over 30 years and has not been conclusively solved to date, getting urgency with the exponential growth of research data, whether it involves demands from funders - the DFG requires 10 years of retention - or digital artifacts that must be preserved indefinitely as digital cultural heritage. Against this background, the integration of the LTA into the RDC of the NFDI is an urgent desideratum in order to be able to guarantee the permanent usability of research data. A distinction must be2 made between the archiving of the digital objects as bitstreams (this can be numeric or textual data or complex objects such as models), which represents a first step towards long-term usability, and the archiving of the semantic and software-technical context of the digital original objects, which entails far more effort. Beyond the technical embedding of the LTA in the system environment of a multi-cloud-based infrastructure, a number of technically differentiated requirements of the NFDI's subject consortia are part of the development of a basic service for the LTA and for the re-use of research data.3 The need for funding for the development of a basic LTA service for the NFDI consortia results primarily from the additional costs associated with the technical and organizational development of a cross-NFDI, decentralized network structure for LTA and the sustainable subsequent use of research data. It is imperative that the technical actors are able to act within the network as a technology-oriented community, and that they can provide their own services as part of the support for also within a federated infrastructure. The working group "Long Term Archiving" (LTA) is to develop the requirements of the technical consortia for LTA and, on this basis, strategic approaches for the implementation of a basic service LTA. The working group consists of members of various NFDI consortia covering the humanities, natural science and engineering disciplines and experts from a variety of pertinent infrastructures with strong overall connections to the nestor long-term archiving competence network. The close linkage of NFDI consortia with experienced4 partners in the field of LTA ensures that a) the relevant technical state-of-the-art is present in the group and b) the knowledge of data producers about contexts of origin and data users interact directly. This composition enables the team to take an overarching view that spans the requirements of the disciplines and consortia, also takes into account interdisciplinary needs, and at the same time brings in the existing know-how in the infrastructure sector.